The database deals purely with proteins found in plasma and
serum. Why was it necessary to create Plasma Proteome Database
(PPD)?

Plasma is the most commonly diagnosed clinical sample. Clinicians can diagnose
pathological conditions by quantification of specific proteins.
Over 9,000 proteins in plasma and serum have thus far been reported
and are only expected to increase with evolving high-resolution
and high-sensitivity protein detection/identification technologies.
Documentation of qualitative and quantitative information on broad
range of proteins in plasma/serum in a user-friendly and queryable
manner is a prerequisite to explore the blood proteome. This is
why the Plasma Proteome Database was created.

2.

What is the information that one can get from Plasma proteome Database?

PPD contains proteins reported in plasma and serum from healthy individuals.
Experimental method employed to identify each protein is also provided.
From studies employing mass spectrometry-based approaches to identify
plasma/serum proteins, information pertaining to the type of mass
spectrometer employed and the proteotypic peptides reported are
available. Quantitative information on plasma/serum proteins from
immunoassays such as ELISA and radioimmuno assay, and mass spectrometry-based
assays such as single reaction monitoring/multiple reaction monitoring
and spectral counting are also available in PPD. All the information
is linked to their corresponding PubMed identifiers. Proteins identified
in plasma exosomes along with other experimental details are also
available in PPD.

3.

Is the protein concentration provided only from healthy individuals?

Yes. Plasma protein levels are provided in healthy conditions as reported in
literature.

4.

What are the applications of PPD?

PPD can be used as a reference database to compare and report proteins or peptides
novel to experimental results obtained by researchers. The proteotypic
peptides cataloged in PPD can be used to design and evaluate proteins
using mass spectrometry both qualitatively and quantitatively. The
list of proteins in PPD can also be used to analyze proteins from
other body fluids. The proteins thus far identified in plasma/serum
would also provide a reference for analysis of cellular secretome,
proteins shed from cell surface and screen for ligands of orphan
receptors. Above all, PPD will enable researchers in biomarker development
to screen candidate molecules that are reported in plasma/serum,
from a larger set of proteins identified in the discovery phase
to pursue further validation.

5.

Can I download data from PPD?

Yes. The data is available for free download in .XML and tab delimited formats
for non-commercial use under Creative Commons License 2.5 which
attributes unrestricted use, distribution, and reproduction in any
medium, provided, adequate credit is given to the authors.

6.

I am from a commercial entity what do I need to do to download the database for
commercial purposes?